GSM7977948: ATAC lungs, Prdm3/16KO, rep2; Mus musculus; ATAC-seq
Lungs from E17.5 mice were harvested, minced, and incubated in RPMI media containing Liberase TM (Roche, 50ug/ml) and DNAse I (MilliporeSigma, 100ug/ml) at 37C for 30min. Tissues were dissociated with GentleMACS cell dissociator, then subjected to RBC lysis buffer for 2min on ice, followed by an incubation with FcR blocking reagent (Miltenyi: 130-092-575) on ice for 10min, followed by an incubation with CD326 anti-Mouse-EpCAM microbeads (Miltenyi: 130-105-958) at 4C for 15min. Cells were subjected to positive selection with an LS column and collected in MACS buffer (Miltenyi). Cells were quantified manually via hemacytometer with trypan blue. 50,000 Epcam+ epithelial cells were captured and nuclei were isolated using lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Nuclei were subjected to a transposition reaction with a Tagment DNA TDE1 Enzyme and Buffer Kit (Illumina) at 37C for 30m. Transposed DNA fragments were quantified by qPCR and amplified with barcoded primers using the NEB Next High-Fidelity 2x PCR master mix. Libraries sent to Genewiz for sequencing